It's not the same thing to strike a joint directly as it is to apply a submission.

That said, it is true that some of these are banned in certain formats for precisely this reason.

But the main difference for me is that a submission hold is intended to get a guy to tap. A direct strike to the knee cap is intended to debilitate the leg, not induce a submission or cause a knockout (the two ways of finishing a fight). Rather, it is to create structural damage which will make the guy less effective. Given the danger and consequences these kicks can have, I don't think they should be allowed.